RetrogeneDB ID: retro_amel_1893

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195343.1:43493..44062(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000002830
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TAGLN3
• Ensembl ID: ENSAMEG00000018148
• Aliases: None
• Description: transgelin 3 [Source:HGNC Symbol;Acc:29868]

Sequence

>retro_amel_1893
ATGGCCAATAGGGTACCTGCCTATGGCCTGAGATAGAAGGTACAACAGAAGATTGAGAAACTGTAGGACACAGACCTGGA
GCAGATCCTGATCTGGTGAGTCACCACCCAGTGCCACAAGCACGTGGGCCCACCCCAGCCTGGGCAGGAGAACTTCCAGA
TTTGGCTTAAGGATGGCACAGTGCTGTGTGAGCTAATCAACGGGCTGTACCCCAAGGGACAAGCCTCAGTGAAGAAGATC
CAGGCCTCCACTATGGCCTTCAAACAGCTGGAGAAGATCTCTGTTCCCTCAGGAGGCCTAGCACTATGGCCTCAAAACTC
ACTGACGTCTTCCAAACTGTGGACCTCTGGGAAGGGAAGAACATGCCATGTATGCAGCAGACGCTGATGAACCTGGGTGG
ACTGGCAGTGGCCCAGGAGGATGGGCTTTTTTCTGGGGATCCCAAATGGTTTCCTAAGAAGTTCAAGGAGAACCCTCGGA
ACTTCTCGGACAACCAGCTGCAAGAGGGCAAGAACATCATTGGGTTGCAGATGGGCATGAACTGCAGGTCATCCCAGGCC
AGCCTGACC

Alignment

ORF - retro_amel_1893 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.88 %
• Parental protein coverage: 93.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MANRGPSYGLSREVQEKIEQKYDADLENKLVDWIILQCAEDIEHPPPGRAHFQKWLMDGTVLCKLINSLY
          MANR.P.YGL...VQ.KIE...D.DLE..L......QC......P.PG...FQ.WL.DGTVLC.LIN.LY
Retrocopy MANRVPAYGLR*KVQQKIEKL*DTDLEQILIW*VTTQCHKHVGPPQPGQENFQIWLKDGTVLCELINGLY

Parental  PPGQEPIPKISESKMAFKQMEQISQ-FLKAAETYGVRTTDIFQTVDLWEGKDMAAVQRTLMALGSVAVTK
          P.GQ....KI..S.MAFKQ.E.IS...L....T.....TD.FQTVDLWEGK.M...Q.TLM.LG..AV..
Retrocopy PKGQASVKKIQASTMAFKQLEKISV<SLRRPSTMASKLTDVFQTVDLWEGKNMPCMQQTLMNLGGLAVAQ

Parental  DDGCYRGEPSWFHRKAQQNRRGFSEEQLRQGQNVIGLQMGSNKGASQAGMT
          .DG...G.P.WF..K...N.R.FS..QL..G.N.IGLQMG.N...SQA..T
Retrocopy EDGLFSGDPKWFPKKFKENPRNFSDNQLQEGKNIIGLQMGMNCRSSQASLT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_1893 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1893 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000062	1 retrocopy	retro_amel_675,
Ailuropoda melanoleuca	ENSAMEG00000016707	1 retrocopy	retro_amel_1412,
Ailuropoda melanoleuca	ENSAMEG00000018148	1 retrocopy	retro_amel_1893 ,